Its been known for quite some time that hydronium ions were out there. Chemically it’s the aqueous cation H3O+, the type of oxonium ion produced by protonation of water. It’s present in some quantity in any solution containing water resulting from two water molecules reacting, but will be present in higher concentrations in more acidic solutions. Hydronium is the common name and the ion is also known as oxonium.

Simply put, a hydronium ion is a water molecule with an extra hydrogen ion attached to it. The molecule turns up in lots of acidic reactions and is thought to have an important role in converting sugars in woody biomass into alcohol, a potential alternative fuel.

Prior to the Los Alamos led research, no one has ever directly witnessed the role of the hydronium ion in macromolecular catalysts – the catalytic mechanisms of enzymes.

The research team took an interest in an enzyme that has potential to allow conversion of sugars in woody biomass because the enzyme loses its effectiveness when the pH value of the milieu is lowered. That is a common occurrence in the interior of industrial yeast cells fermenting alcohol, not something commercial scale production and high efficiency will tolerate for long. Lots of expensive yeast is not reaching its full productivity and new expensive yeast is being added.

The researchers discovered a crucial change as the system they were studying fell into the acidic range of the pH scale (below 6). The hydronium ion that could be seen facilitating the binding of a metal ion cofactor crucial to the conversion of the sugar molecule into its fermentable form suddenly became dehydrated – think of water, H2O, being removed from hydronium, H3O+. The space occupied by the relatively large hydronium ion collapsed into a tiny volume occupied by the remaining proton (a positively charged hydrogen ion, H+). This spatial change in the molecular structure prevented the sugar from being attacked by the enzyme.

That’s a major key to efficiency. The team’s observation provides an answer about why pH plays such an important role in fermentation and how acidity renders the enzyme inactive. Most importantly the team has shown that the hydronium ion plays a key role in the transport of protons in these types of biochemical systems.

Previous researchers had attempted to use X-rays to understand the chemical mechanism of enzymes, but no one has ever directly witnessed the role of the hydronium ion. This is because tiny hydrogen atoms are essentially invisible under X-rays. To help make things visible, the Los Alamos team substituted hydrogen in their enzyme samples with deuterium, an isotope of hydrogen that behaves chemically identical to its nonisotopic counterpart. Deuterium yields a clear signal when bombarded with neutrons. The neutrons provided a perfect method for uncloaking the elusive hydronium ions, which appeared as a pyramid-shaped mass in the enzyme’s active site where the chemical reaction occurs.

Los Alamos researcher Andrey Kovalevsky, principal author of the paper said, “This is something that has never been seen before. This proves that hydronium is the active chemical agent in our studies of the catalytic mechanism of enzymes.”

It’s likely that hydronium will be more intensely studied now that the activity can be seen. The research has broad biological implications particularly in metabolic systems.

We’re witnessing what could be a breakthrough in biological process for fuel production. Of late the chemical processes seem to be gaining ground with oxidation or simply burning biomass, pyrolysis, and other chemical processes looking very attractive. As Al Fin found at Green Car Congress few days ago, one leading means to use the biomass energy in algae was the bluntest instrument – combustion produces the largest energy release to make electricity.

While that may be fine, the real world trials haven’t started just yet. And time is something the world has to work out finding the most useful way to use biomass carbon and hydrogen molecules in what hopes would be an endlessly recycling fuel supply.

Simply drying algae and burning it wholesale seems just a bit too simplistic. Surely science can do better than that. Getting a handle on hydronium, understanding how to use it most effectively may offer biology a chance to come up with a better solution.

Algae Process Comparison from the University of Virginia. Click image for the largest view.

The needs of the future will decide how best to use biomass – in electric power generation or liquid fuels. Yet the University of Virginia’s study of algae’s potential use as a transportation energy source is instructive – process paths will matter as biomass is used in more to the future’s energy mixture.